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[ptb_ptb]

Yeah, so I noticed that there are a lot of trees in caverns that have their trunk underwater. Is that expected, or a bug?

It does make them awkward to fell.

[Rum]

Seeing as they are all mystical large mushrooms and fungus, this seems intended.

[samanato]

Mushroom trees have [BIOME:SUBTERRANEAN_WATER], which is also the biome of cave fish and pond grabbers among other things.  Interestingly, putting a tree in any watery biome, like a lake, will make it grow underwater.

Worth noting, that the previous version also had underwater cavern trees, they were just harder to notice because they were totally submerged.

[Fat Friar]

Can confirm the above. I once had to move an entire well shaft a tile to the left when I found it wouldn't draw from the underground lake, due to a fungiwood sitting submerged in the tile under the well.